Hello everyone, I'm rather a beginner to bioinformatics with background mainly in molecular biology (wet labs).
I have a project where I must align thousands of HIV1 genomes and the tool I found perfect for the job was Mugsy, I spent few weeks understanding it and get it to work. I tested it to align 2, 5 , 10 and 50 and the results were perfect however now I must align 13K genomes.
I'm using a server with 128gb RAM and shouldn't face any technical/memory related issues however the terminal command for running mugsy requires I type all input files, typing 13K file names is quite impractical and with I tried to copy-pasta file names in notepad and paste it to the terminal it just too long for a single terminal page and cuts the line in between. I tried combining all the genomes in a single multi-fasta file however mugsy detected only the first genome.
Any ways I could input a directory rather than a single file into mugsy or any suggestion how i could kick mugsy to detect all the genomes in a multi-fasta file ? Any help would be really appreciated, I tried searching the forum for similar issues but couldn't find any, thanks in advance for any help :)